com.milaboratory.mitools.trimmer

Class SequenceTrimmer

java.lang.Object

com.milaboratory.mitools.trimmer.SequenceTrimmer

All Implemented Interfaces:

cc.redberry.pipe.Processor<com.milaboratory.core.io.sequence.SingleRead,com.milaboratory.core.io.sequence.SingleRead>, Serializable

public final class SequenceTrimmer
extends Object
implements cc.redberry.pipe.Processor<com.milaboratory.core.io.sequence.SingleRead,com.milaboratory.core.io.sequence.SingleRead>, Serializable

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
SequenceTrimmer(int qualityToTrimm, boolean trimmLeft, boolean trimmRight)

Method Summary

Methods

Modifier and Type	Method and Description
long	getTotalTrimmedReads()
long	getTrimmedNucleotidesLeft()
long	getTrimmedNucleotidesRight()
long	getTrimmedReadsLeft()
long	getTrimmedReadsRight()
com.milaboratory.core.io.sequence.SingleRead	process(com.milaboratory.core.io.sequence.SingleRead input)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SequenceTrimmer

public SequenceTrimmer(int qualityToTrimm,
               boolean trimmLeft,
               boolean trimmRight)

Method Detail

getTrimmedNucleotidesLeft

public long getTrimmedNucleotidesLeft()

getTrimmedReadsLeft

public long getTrimmedReadsLeft()

getTrimmedNucleotidesRight

public long getTrimmedNucleotidesRight()

getTrimmedReadsRight

public long getTrimmedReadsRight()

getTotalTrimmedReads

public long getTotalTrimmedReads()

process

public com.milaboratory.core.io.sequence.SingleRead process(com.milaboratory.core.io.sequence.SingleRead input)

Specified by:

process in interface cc.redberry.pipe.Processor<com.milaboratory.core.io.sequence.SingleRead,com.milaboratory.core.io.sequence.SingleRead>